Extended Data Fig. 2: Global properties of gene expression during brain development.

a, Erythrocyte clusters expressing Hbb-bh1 (>500 UMIs per cell) (primitive erythropoiesis) or Hbb-bs (>5,000 UMIs per cell) (definitive erythropoiesis). b, Histogram of cell cycle scores (left) and cell cycle scores indicated on the main t-SNE (right). c, Distribution of total UMIs per cell. d, Distribution of total number of genes detected per cell. e, Distribution of the fraction of unspliced reads detected per cell. f, Average z score for a set of genes with GO term related to the spliceosome. g, Number of clusters observed for each major cell class, as a function of varying hyper-parameters of the clustering algorithm (indicated, left). Top row shows the default clustering. Each subsequent row varies one or more hyper-parameters (number of genes selected, number of HPF components and the stop condition), resulting in different numbers of clusters per class. Deviations from the default settings are indicated by the colours. h, Confusion matrix comparing clustering results for neurons using default settings (vertical axis) and clustering using only 500 genes (horizontal axis). i, Same as h, but for radial glia. The expression of key marker genes is indicated along the axes to reveal major subclasses. j, Distribution of major classes of cells by gestational age.